S. A. Ogurtsov, A. Y. Rogozin, I. B. Koonin, E. V. Lipman, and D. J. , Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals, Nucleic Acids Res, vol.32, pp.1774-1782, 2004.

M. Shehu-xhilaga, S. M. Crowe, and J. Mak, Maintenance of the Gag/Gag-Pol Ratio Is Important for Human Immunodeficiency Virus Type 1 RNA Dimerization and Viral Infectivity, Journal of Virology, vol.75, issue.4, pp.1834-1841, 2001.
DOI : 10.1128/JVI.75.4.1834-1841.2001

Y. Shibagaki, N. Itoh, H. Yamada, S. Nagata, and K. Mizumoto, mRNA capping enzyme. Isolation and characterization of the gene encoding mRNA guanylytransferase subunit from Saccharomyces cerevisiae, J Biol Chem, vol.267, pp.9521-9528, 1992.

J. M. Skuzeski, L. M. Nichols, R. F. Gesteland, and J. F. Atkins, The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons, Journal of Molecular Biology, vol.218, issue.2, pp.365-373, 1991.
DOI : 10.1016/0022-2836(91)90718-L

P. Somogyi, A. J. Jenner, I. Brierley, and S. C. Inglis, Ribosomal pausing during translation of an RNA pseudoknot., Molecular and Cellular Biology, vol.13, issue.11, pp.6931-6940, 1993.
DOI : 10.1128/MCB.13.11.6931

H. Song, P. Mugnier, A. K. Das, H. M. Webb, D. R. Evans et al., The Crystal Structure of Human Eukaryotic Release Factor eRF1???Mechanism of Stop Codon Recognition and Peptidyl-tRNA Hydrolysis, Cell, vol.100, issue.3, pp.311-321, 2000.
DOI : 10.1016/S0092-8674(00)80667-4

C. M. Spahn, R. Beckmann, N. Eswar, P. A. Penczek, A. Sali et al., Structure of the 80S Ribosome from Saccharomyces cerevisiae???tRNA-Ribosome and Subunit-Subunit Interactions, Cell, vol.107, issue.3, pp.373-386, 2001.
DOI : 10.1016/S0092-8674(01)00539-6

C. M. Spahn, M. G. Gomez-lorenzo, R. A. Grassucci, R. Jorgensen, G. R. Andersen et al., Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation, The EMBO Journal, vol.23, issue.5, pp.1008-1019, 2004.
DOI : 10.1038/sj.emboj.7600102

C. M. Spahn and K. H. Nierhaus, Models of the elongation cycle: an evaluation, Biol Chem, vol.3799705140, pp.753-772, 1998.

G. Srinivasan, C. M. James, and J. A. Krzycki, Pyrrolysine Encoded by UAG in Archaea: Charging of a UAG-Decoding Specialized tRNA, Science, vol.296, issue.5572, pp.1459-1462, 2002.
DOI : 10.1126/science.1069588

I. Stansfield and M. F. Tuite, Polypeptide chain termination in Saccharomyces cerevisiae, Current Genetics, vol.34, issue.5, pp.385-395, 1994.
DOI : 10.1007/BF00351776

L. Su, L. Chen, M. Egli, J. M. Berger, R. et al., Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot, Nat Struct Biol, vol.6, pp.285-292, 1999.

D. Sung and H. Kang, Mutational analysis of the RNA pseudoknot involved in efficient ribosomal frameshifting in simian retrovirus-1, Nucleic Acids Research, vol.26, issue.6, pp.1369-1372, 1998.
DOI : 10.1093/nar/26.6.1369

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

S. R. Eddy, Profile hidden Markov models, Bioinformatics, vol.14, issue.9, pp.755-763, 1998.
DOI : 10.1093/bioinformatics/14.9.755

T. Kulikova, P. Aldebert, N. Althorpe, W. Baker, K. Bates et al., The EMBL Nucleotide Sequence Database, Nucleic Acids Research, vol.32, issue.90001, pp.27-30, 2004.
DOI : 10.1093/nar/gkh120

URL : https://hal.archives-ouvertes.fr/hal-00427196

N. J. Mulder, R. Apweiler, T. K. Attwood, A. Bairoch, D. Barrell et al., The InterPro Database, 2003 brings increased coverage and new features, Nucleic Acids Research, vol.31, issue.1, pp.315-318, 2003.
DOI : 10.1093/nar/gkg046

URL : https://hal.archives-ouvertes.fr/hal-01214149

R. J. Mural, Software review, Briefings in Bioinformatics, vol.1, issue.2, pp.199-200, 2000.
DOI : 10.1093/bib/1.2.199

J. E. Stajich, D. Block, K. Boulez, S. E. Brenner, S. A. Chervitz et al., The Bioperl Toolkit: Perl Modules for the Life Sciences, Genome Research, vol.12, issue.10, pp.1611-1618, 2002.
DOI : 10.1101/gr.361602

E. M. Zdobnov and R. Apweiler, InterProScan - an integration platform for the signature-recognition methods in InterPro, Bioinformatics, vol.17, issue.9, pp.847-848, 2001.
DOI : 10.1093/bioinformatics/17.9.847

R. K. Agrawal, R. K. Lata, and J. Frank, Conformational variability in Escherichia coli 70S ribosome as revealed by 3D cryo-electron microscopy, The International Journal of Biochemistry & Cell Biology, vol.31, issue.1, pp.243-254, 1999.
DOI : 10.1016/S1357-2725(98)00149-6

P. V. Baranov, R. F. Gesteland, and J. F. Atkins, P-site tRNA is a crucial initiator of ribosomal frameshifting, RNA, vol.10, issue.2, pp.221-230, 2004.
DOI : 10.1261/rna.5122604

M. Bekaert, L. Bidou, A. Denise, G. Duchateau-nguyen, J. P. Forest et al., Towards a computational model for -1 eukaryotic frameshifting sites, Bioinformatics, vol.19, issue.3, pp.327-335, 2003.
DOI : 10.1093/bioinformatics/btf868

I. Brierley, A. J. Jenner, and S. C. Inglis, Mutational analysis of the ???slippery-sequence??? component of a coronavirus ribosomal frameshifting signal, Journal of Molecular Biology, vol.227, issue.2, pp.463-479, 1992.
DOI : 10.1016/0022-2836(92)90901-U

I. Brierley, M. R. Meredith, A. J. Bloys, and T. G. Hagervall, Expression of a coronavirus ribosomal frameshift signal in Escherichia coli: influence of tRNA anticodon modification on frameshifting, Journal of Molecular Biology, vol.270, issue.3, pp.360-373, 1997.
DOI : 10.1006/jmbi.1997.1134

Y. Fukunishi and Y. Hayashizaki, Amino acid translation program for fulllength cDNA sequences with frameshift errors, Physiol Genomics, vol.5, pp.81-87, 2001.

A. B. Hammell, R. C. Taylor, S. W. Peltz, and J. D. Dinman, Identification of putative programmed -1 ribosomal frameshift signals, 1999.

P. Harrison, A. Kumar, N. Lan, N. Echols, M. Snyder et al., A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution, Journal of Molecular Biology, vol.316, issue.3, pp.409-419, 2002.
DOI : 10.1006/jmbi.2001.5343

T. Jacks, H. D. Madhani, F. R. Masiarz, and H. E. Varmus, Signals for ribosomal frameshifting in the rous sarcoma virus gag-pol region, Cell, vol.55, issue.3, pp.447-458, 1988.
DOI : 10.1016/0092-8674(88)90031-1

Y. G. Kim, S. Maas, R. , and A. , Comparative mutational analysis of cis-acting RNA signals for translational frameshifting in HIV-1 and HTLV-2, Nucleic Acids Research, vol.29, issue.5, pp.1125-1131, 2001.
DOI : 10.1093/nar/29.5.1125

M. Leger, S. Sidani, and L. Brakier-gingras, A reassessment of the response of the bacterial ribosome to the frameshift stimulatory signal of the human immunodeficiency virus type 1, RNA, vol.10, issue.8, pp.1225-1235, 2004.
DOI : 10.1261/rna.7670704

J. Liphardt, The mechanism of -1 ribosomal frameshifting: experimental and theoretical analysis, 1999.

J. D. Lopinski, J. D. Dinman, and J. A. And-bruenn, Kinetics of Ribosomal Pausing during Programmed -1 Translational Frameshifting, Molecular and Cellular Biology, vol.20, issue.4, pp.1095-1103, 2000.
DOI : 10.1128/MCB.20.4.1095-1103.2000

G. Oshiro, L. M. Wodicka, M. P. Washburn, J. R. Yates, D. J. Lockhart et al., Parallel Identification of New Genes in Saccharomyces cerevisiae, Genome Research, vol.12, issue.8, pp.1210-1220, 2002.
DOI : 10.1101/gr.226802

E. P. Plant, K. L. Jacobs, J. W. Harger, A. Meskauskas, J. L. Jacobs et al., The 9-A solution: How mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting, RNA, vol.9, issue.2, pp.168-174, 2003.
DOI : 10.1261/rna.2132503

M. Sato, H. Umeki, R. Saito, A. Kanai, and M. Tomita, Computational analysis of stop codon readthrough in D.melanogaster, Bioinformatics, vol.19, issue.11, pp.1371-1380, 2003.
DOI : 10.1093/bioinformatics/btg183

P. Somogyi, A. J. Jenner, I. Brierley, and S. C. Inglis, Ribosomal pausing during translation of an RNA pseudoknot., Molecular and Cellular Biology, vol.13, issue.11, pp.6931-6940, 1993.
DOI : 10.1128/MCB.13.11.6931

S. L. Wolin and P. Walter, Ribosome pausing and stacking during translation of a eukaryotic mRNA, Embo J, vol.7, pp.3559-3569, 1988.

E. Yelverton, D. Lindsley, P. Yamauchi, and J. A. Gallant, The function of a ribosomal frameshifting signal from human immunodeficiency virus-1 in Escherichia coli, Molecular Microbiology, vol.76, issue.2, pp.303-313, 1994.
DOI : 10.1016/0092-8674(88)90260-7

R. Baranov, P. Gurvich, O. Fayet, O. Prere, M. Miller et al., RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression, Nucleic Acids Research, vol.29, issue.1, pp.264-267, 2001.
DOI : 10.1093/nar/29.1.264

C. Bertrand, M. Prere, R. Gesteland, J. Atkins, and O. Fayet, Influence of the stacking potential of the base 3??? of tandem shift codons on ???1 ribosomal frameshifting used for gene expression, RNA, vol.8, issue.1, pp.16-28, 2002.
DOI : 10.1017/S1355838202012086

L. Bidou, G. Stahl, I. Hatin, O. Namy, J. Rousset et al., Nonsense-mediated decay mutants do not affect programmed ???1 frameshifting, RNA, vol.6, issue.7, pp.952-961, 2000.
DOI : 10.1017/S1355838200000443

F. Van-batenburg, A. Gultyaev, C. Pleij, J. L. Olienhoek, J. H. Friedman et al., PseudoBase: a database with RNA pseudoknots, Nucleic Acids Research, vol.28, issue.1, pp.201-204, 1984.
DOI : 10.1093/nar/28.1.201

I. Brierley, Ribosomal frameshifting on viral RNAs, Journal of General Virology, vol.76, issue.8, pp.1885-1892, 1995.
DOI : 10.1099/0022-1317-76-8-1885

I. Brierley, N. J. Rolley, A. J. Jenner, and S. C. Inglis, Mutational analysis of the RNA pseudoknot component of a coronavirus ribosomal frameshifting signal, Journal of Molecular Biology, vol.220, issue.4, pp.889-902, 1991.
DOI : 10.1016/0022-2836(91)90361-9

I. Brierley, A. J. Jenner, and S. C. Inglis, Mutational analysis of the ???slippery-sequence??? component of a coronavirus ribosomal frameshifting signal, Journal of Molecular Biology, vol.227, issue.2, pp.463-479, 1992.
DOI : 10.1016/0022-2836(92)90901-U

L. X. Chen and I. Tinoco, The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus, J. Mol. Biol, vol.247, pp.963-978, 1995.

X. Chen, H. Kang, L. X. Shen, M. Chamorro, H. E. Varmus et al., A characteristic bent conformation of RNA pseudoknots promotes ?1 frameshifting during translation of retroviral RNA Identification and analysis of the pseudo-knot containing gag-pro ribosomal frameshift signal of simian retrovirus ?1, Analysis of the role of the pseudoknot component in the SRV-1 gag-pro ribosomal frameshift signal: loop lengths and stability of the stem regions, pp.479-483, 1994.

J. D. Dinman, T. Icho, and R. B. Wickner, A ?1 ribosomal frameshift in a double-stranded RNA virus of yeast forms a gagpol fusion domain, Proc. Natl Acad. Sci. USA, pp.174-178, 1991.

J. Dinman, M. Ruiz-echevarria, and S. Peltz, Translating old drugs into new treatments: ribosomal frameshifting as a target for antiviral agents, Trends in Biotechnology, vol.16, issue.4, pp.190-196, 1998.
DOI : 10.1016/S0167-7799(97)01167-0

B. Dujon, D. Alexandraki, B. Andre, W. Ansorge, V. Baladron et al., Complete DNA sequence of yeast chromosome XI, Nature, vol.369, issue.6479, pp.371-378, 1994.
DOI : 10.1038/369371a0

P. Farabaugh, Programmed translational frameshifting. Microbiological review, pp.103-134, 1996.
DOI : 10.1146/annurev.genet.30.1.507

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC239420

R. Gesteland and J. Atkins, Recoding: Dynamic Reprogramming of Translation, Annual Review of Biochemistry, vol.65, issue.1, pp.741-768, 1996.
DOI : 10.1146/annurev.bi.65.070196.003521

R. Gesteland, R. Weiss, and J. F. Atkins, Recoding: reprogrammed genetic decoding, Science, vol.257, issue.5077, pp.1640-1641, 1992.
DOI : 10.1126/science.1529352

D. P. Giedroc, C. A. Theimer, and P. L. Nixon, Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting, Journal of Molecular Biology, vol.298, issue.2, pp.167-185, 2000.
DOI : 10.1006/jmbi.2000.3668

A. Goffeau, B. Barrell, H. Bussey, R. Davis, B. Dujon et al., Life with 6000 Genes, Science, vol.274, issue.5287, pp.563-567, 1996.
DOI : 10.1126/science.274.5287.546

A. B. Hammell, R. C. Taylor, S. W. Peltz, and J. D. Dinman, Identification of putative programmed ?1 ribosomal frameshift signals in large DNA databases, Genome Res, vol.9, pp.417-427, 1999.

T. Jacks and H. Varmus, Expression of the Rous sarcoma virus pol gene by ribosomal frameshifting, Science, vol.230, issue.4731, pp.1237-1242, 1985.
DOI : 10.1126/science.2416054

T. Jacks, M. Power, F. Masiarz, P. Luciw, P. Barr et al., Characterization of ribosomal frameshifting in HIV-1 gag-pol expression, Nature, vol.331, issue.6153, pp.280-283, 1988.
DOI : 10.1038/331280a0

H. Kang, J. V. Hines, and I. Tinoco, Conformation of a Non-frameshifting RNA Pseudoknot from Mouse Mammary Tumor Virus, Journal of Molecular Biology, vol.259, issue.1, pp.135-147, 1996.
DOI : 10.1006/jmbi.1996.0308

Y. Kim, L. Su, S. Maas, A. Neill, and A. Rich, Specific mutations in a viral RNA pseudoknot drastically change ribosomal frameshifting efficiency, Proc. Natl Acad. Sci. USA, pp.14234-14239, 1999.
DOI : 10.1006/jmbi.1998.1812

H. Kollmus, M. Hentze, and H. Hauser, Regulated ribosomal frameshifting by an rna-protein interaction, RNA, vol.2, pp.316-323, 1996.

H. Kontos, S. Napthine, and I. Brierley, Ribosomal Pausing at a Frameshifter RNA Pseudoknot Is Sensitive to Reading Phase but Shows Little Correlation with Frameshift Efficiency, Molecular and Cellular Biology, vol.21, issue.24, pp.8657-8670, 2001.
DOI : 10.1128/MCB.21.24.8657-8670.2001

J. Liphardt, The mechanism of ?1 ribosomal frameshifting: experimental and theoretical analysis, 1999.

J. Lopinski, J. Dinman, and J. Bruenn, Kinetics of Ribosomal Pausing during Programmed -1 Translational Frameshifting, Molecular and Cellular Biology, vol.20, issue.4, pp.1095-1103, 2000.
DOI : 10.1128/MCB.20.4.1095-1103.2000

B. Marczinke, R. Fisher, M. Vidakovic, A. Bloys, and I. Brierley, Secondary structure and mutational analysis of the ribosomal frameshift signal of rous sarcoma virus, Journal of Molecular Biology, vol.284, issue.2, pp.205-225, 1998.
DOI : 10.1006/jmbi.1998.2186

C. Medigue, M. Rose, A. Viari, and A. Danchin, Detecting and Analyzing DNA Sequencing Errors: Toward a Higher Quality of the Bacillus subtilis Genome Sequence, Genome Research, vol.9, issue.11, pp.1116-1127, 1999.
DOI : 10.1101/gr.9.11.1116

N. Mejlhede, J. Atkins, and J. Neuhard, Ribosomal ?1 frameshifting during decoding of Bacillus subtilis cdd occurs at the sequence CGA AAG, J. Bacteriol, vol.181, pp.2930-2937, 1999.

O. Namy, I. Hatin, and J. P. Rousset, Impact of the six nucleotides downstream of the stop codon on translation termination, EMBO reports, vol.23, issue.9, pp.787-793, 2001.
DOI : 10.1093/embo-reports/kve176

S. Napthine, J. Liphardt, A. Bloys, S. Routledge, and I. Brierley, The role of RNA pseudoknot stem 1 length in the promotion of efficient ???1 ribosomal frameshifting, Journal of Molecular Biology, vol.288, issue.3, pp.305-320, 1999.
DOI : 10.1006/jmbi.1999.2688

J. Quinlan, C4.5: Programs for machine learning, 1993.

K. Shigemoto, J. Brennan, E. Walls, C. Watson, D. Stott et al., Identification and characterisation of a developmentally regulated mammalian gene that utilises ???1 programmed ribosomal frameshifting, Nucleic Acids Research, vol.29, issue.19, pp.4079-4088, 2001.
DOI : 10.1093/nar/29.19.4079

P. Somogyi, A. J. Jenner, I. Brierley, and S. C. Inglis, Ribosomal pausing during translation of an RNA pseudoknot., Molecular and Cellular Biology, vol.13, issue.11, pp.6931-6940, 1993.
DOI : 10.1128/MCB.13.11.6931

A. Srinivasan, R. King, and D. Bristol, An assessment of submissions made to the Predictive Toxicology Evaluation Challenge, Proceedings of the Sixteenth International Joint Conference on Artificial Intelligence (IJCAI-99), 1999.

F. Torre, Intégration des biais de langagè a l'algorithme générer-et-tester?Contributionsàtester?Contributions`tester?Contributionsà l'apprentissage disjonctif, 2000.

Z. Tsuchihashi and A. Kornberg, Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme., Proc. Natl Acad. Sci. USA, pp.2516-2520, 1990.
DOI : 10.1073/pnas.87.7.2516

C. Tu, T. Tzeng, and J. A. Bruenn, Ribosomal movement impeded at a pseudoknot required for frameshifting., Proc. Natl Acad. Sci. USA, pp.8636-8640, 1992.
DOI : 10.1073/pnas.89.18.8636

I. H. Witten and E. Frank, Data mining, ACM SIGMOD Record, vol.31, issue.1, 2000.
DOI : 10.1145/507338.507355

E. Yelverton, D. Lindsley, P. Yamauchi, and J. Gallant, The function of a ribosomal frameshifting signal from human immunodeficiency virus-1 in Escherichia coli, Molecular Microbiology, vol.76, issue.2, pp.303-313, 1994.
DOI : 10.1016/0092-8674(88)90260-7

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

P. V. Baranov, R. F. Gesteland, and J. F. Atkins, Recoding: translational bifurcations in gene expression, Gene, vol.286, issue.2, pp.187-201, 2002.
DOI : 10.1016/S0378-1119(02)00423-7

P. V. Baranov, R. F. Gesteland, and J. F. Atkins, Release factor 2 frameshifting sites in different bacteria, EMBO Reports, vol.3, issue.4, pp.373-377, 2002.
DOI : 10.1093/embo-reports/kvf065

C. Bertrand, M. F. Prere, R. F. Gesteland, J. F. Atkins, and O. Fayet, Influence of the stacking potential of the base 3??? of tandem shift codons on ???1 ribosomal frameshifting used for gene expression, RNA, vol.8, issue.1, pp.16-28, 2002.
DOI : 10.1017/S1355838202012086

L. Bidou, G. Stahl, I. Hatin, O. Namy, J. P. Rousset et al., Nonsense-mediated decay mutants do not affect programmed ???1 frameshifting, RNA, vol.6, issue.7, pp.952-961, 2000.
DOI : 10.1017/S1355838200000443

E. Birney, J. D. Thompson, and T. J. Gibson, PairWise and SearchWise: Finding the Optimal Alignment in a Simultaneous Comparison of a Protein Profile against All DNA Translation Frames, Nucleic Acids Research, vol.24, issue.14, pp.2730-2739, 1996.
DOI : 10.1093/nar/24.14.2730

M. Borodovsky and J. Mcininch, Recognition of genes in DNA sequence with ambiguities, Biosystems, vol.30, issue.1-3, pp.161-171, 1993.
DOI : 10.1016/0303-2647(93)90068-N

I. Brierley, P. Digard, and S. C. Inglis, Characterization of an efficient coronavirus ribosomal frameshifting signal: Requirement for an RNA pseudoknot, Cell, vol.57, issue.4, pp.537-547, 1989.
DOI : 10.1016/0092-8674(89)90124-4

C. Burge and S. Karlin, Prediction of complete gene structures in human genomic DNA, Journal of Molecular Biology, vol.268, issue.1, 1997.
DOI : 10.1006/jmbi.1997.0951

A. Denise, Y. Ponty, and M. Termier, Random generation of structured genomic sequences. Paper presented at, p.3, 2003.

M. S. Gelfand, A. A. Mironov, and P. A. Pevzner, Gene recognition via spliced sequence alignment., Proceedings of the National Academy of Sciences, vol.93, issue.17, pp.9061-9066, 1996.
DOI : 10.1073/pnas.93.17.9061

R. F. Gesteland, R. B. Weiss, and J. F. Atkins, Recoding: reprogrammed genetic decoding, Science, vol.257, issue.5077, pp.1640-1641, 1992.
DOI : 10.1126/science.1529352

H. Hamada, M. G. Petrino, T. Kakunaga, M. Seidman, and B. D. Stollar, Characterization of genomic poly(dT-dG).poly(dC-dA) sequences: structure, organization, and conformation., Molecular and Cellular Biology, vol.4, issue.12, pp.2610-2621, 1984.
DOI : 10.1128/MCB.4.12.2610

A. B. Hammell, R. C. Taylor, S. W. Peltz, and J. D. Dinman, Identification of putative programmed -1 ribosomal frameshift signals in large DNA databases, Genome Res, vol.9, pp.417-427, 1999.

P. Harrison, A. Kumar, N. Lan, N. Echols, M. Snyder et al., A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution, Journal of Molecular Biology, vol.316, issue.3, pp.409-419, 2002.
DOI : 10.1006/jmbi.2001.5343

H. Ito, Y. Fukuda, K. Murata, and A. Kimura, Transformation of intact yeast cells treated with alkali cations, J Bacteriol, vol.153, pp.163-168, 1983.

T. Jacks, H. D. Madhani, F. R. Masiarz, and H. E. Varmus, Signals for ribosomal frameshifting in the rous sarcoma virus gag-pol region, Cell, vol.55, issue.3, pp.447-458, 1988.
DOI : 10.1016/0092-8674(88)90031-1

T. Jacks and H. E. Varmus, Expression of the Rous sarcoma virus pol gene by ribosomal frameshifting, Science, vol.230, issue.4731, pp.1237-1242, 1985.
DOI : 10.1126/science.2416054

J. Liphardt, The mechanism of -1 ribosomal frameshifting: experimental and theoretical analysis, 1999.

D. R. Maglott, K. S. Katz, H. Sicotte, and K. D. Pruitt, NCBI's LocusLink and RefSeq, Nucleic Acids Research, vol.28, issue.1, pp.126-128, 2000.
DOI : 10.1093/nar/28.1.126

A. A. Mironov, M. A. Roytberg, P. A. Pevzner, G. , and M. S. , Performance-Guarantee Gene Predictions via Spliced Alignment, Genomics, vol.51, issue.3, pp.332-339, 1998.
DOI : 10.1006/geno.1998.5251

N. J. Mulder, R. Apweiler, T. K. Attwood, A. Bairoch, D. Barrell et al., The InterPro Database, 2003 brings increased coverage and new features, Nucleic Acids Research, vol.31, issue.1, pp.315-318, 2003.
DOI : 10.1093/nar/gkg046

URL : https://hal.archives-ouvertes.fr/hal-01214149

O. Namy, G. Duchateau-nguyen, I. Hatin, S. Hermann-le-denmat, M. Termier et al., Identification of stop codon readthrough genes in Saccharomyces cerevisiae, Nucleic Acids Research, vol.31, issue.9, pp.2289-2296, 2003.
DOI : 10.1093/nar/gkg330

O. Namy, J. P. Rousset, S. Napthine, and I. Brierley, Reprogrammed Genetic Decoding in Cellular Gene Expression, Molecular Cell, vol.13, issue.2, pp.157-168, 2004.
DOI : 10.1016/S1097-2765(04)00031-0

M. Sato, H. Umeki, R. Saito, A. Kanai, and M. Tomita, Computational analysis of stop codon readthrough in D.melanogaster, Bioinformatics, vol.19, issue.11, pp.1371-1380, 2003.
DOI : 10.1093/bioinformatics/btg183

K. Shigemoto, J. Brennan, E. Walls, C. J. Watson, D. Stott et al., Identification and characterisation of a developmentally regulated mammalian gene that utilises ???1 programmed ribosomal frameshifting, Nucleic Acids Research, vol.29, issue.19, pp.4079-4088, 2001.
DOI : 10.1093/nar/29.19.4079

E. E. Snyder and G. D. Stormo, Identification of Protein Coding Regions In Genomic DNA, Journal of Molecular Biology, vol.248, issue.1, pp.1-18, 1995.
DOI : 10.1006/jmbi.1995.0198

V. Solovyev and A. Salamov, The Gene-Finder computer tools for analysis of human and model organisms genome sequences, Proc Int Conf Intell Syst Mol Biol, vol.5, pp.294-302, 1997.

V. V. Solovyev, A. A. Salamov, L. , and C. B. , Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames, Nucleic Acids Research, vol.22, issue.24, pp.5156-5163, 1994.
DOI : 10.1093/nar/22.24.5156

G. Stahl, L. Bidou, J. P. Rousset, and M. Cassan, Versatile vectors to study recoding: conservation of rules between yeast and mammalian cells, Nucleic Acids Research, vol.23, issue.9, pp.1557-1560, 1995.
DOI : 10.1093/nar/23.9.1557

J. E. Stajich, D. Block, K. Boulez, S. E. Brenner, S. A. Chervitz et al., The Bioperl Toolkit: Perl Modules for the Life Sciences, Genome Research, vol.12, issue.10, pp.1611-1618, 2002.
DOI : 10.1101/gr.361602

Z. Tsuchihashi and A. Kornberg, Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme., Proceedings of the National Academy of Sciences, vol.87, issue.7, pp.2516-2520, 1990.
DOI : 10.1073/pnas.87.7.2516

E. M. Zdobnov and R. Apweiler, InterProScan - an integration platform for the signature-recognition methods in InterPro, Bioinformatics, vol.17, issue.9, pp.847-848, 2001.
DOI : 10.1093/bioinformatics/17.9.847

D. A. Benson, I. Karsch-mizrachi, D. J. Lipman, J. Ostell, W. et al., GenBank: update, Database issue, pp.23-26, 2004.
DOI : 10.1093/nar/gkh045

URL : http://doi.org/10.1093/nar/gkh045

B. Bos, H. W. Lie, C. Lilley, and I. Jacobs, Cascading Style Sheets, level 2. Available at: http://www, 1998.

P. M. Howley, M. A. Israel, M. F. Law, and M. A. Martin, A rapid method for detecting and mapping homology between heterologous DNAs. Evaluation of polyomavirus genomes, J Biol Chem, vol.254, pp.4876-4883, 1979.